The Distribution and Origins of Pyrus hopeiensis-“Wild Plant With Tiny Population” Using Whole Genome Resequencing

Abstract

<i>Pyrus hopeiensis</i> is a valuable but endangered wild resource in the genus <i>Pyrus</i>. It has been listed as one of the 120 wild species with tiny population in China. The specie has been little studied. A preliminary study of propagation modes in <i>P. hopeiensis</i> was performed through seed propagation, hybridization, self-crossing trials, bud grafting, branch grafting, and investigations of natural growth. The results showed that the population size of <i>P. hopeiensis</i> was very small, the distribution range was limited, and the habitat was extremely degraded. In the wild population, natural hybridization and root tiller production were the major modes of propagation. Whole genome re-sequencing of the 23 wild and cultivated accessions from <i>Pyrus</i> species collected was performed using an Illumina HiSeq sequencing platform. The sequencing depth range was 26.56x-44.85x and the average sequencing depth was 32x. Phylogenetic tree and principal component analyses (PCA) based on SNPs showed that the wild <i>Pyrus</i> species, such as PWH06, PWH07, PWH09, PWH10, PWH13, and PWH17, were closely related to both <i>P. hopeiensis</i> HB-1 and <i>P. hopeiensis</i> HB-2. Using these results in combination with morphological characteristics, it speculated that <i>P. hopeiensis</i> populations may form a natural hybrid group with frequent gene exchanges between and within groups. A selective elimination analysis on the <i>P. hopeiensis</i> population were performed using Fst and π radio and a total of 381 overlapping genes including <i>SAUR72, IAA20, HSFA2</i>, and <i>RKP</i> genes were obtained. These genes were analyzed by gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) function enrichment. And four KEGG pathways, including lysine degradation, sphingolipid metabolism, other glycan degradation, and betaine biosynthesis were significantly enriched in the <i>P. hopeiensis</i> population. Our study provided information on genetic variation, evolutionary relationships, and gene enrichment in <i>P. hopeiensis</i> population. These data will help reveal the evolutionary history and origin of <i>P. hopeiensis</i> and provide guidelines for subsequent research on the locations of functional genes.